The navigation data of the Amundsen scientific expeditions between 2003 and 2023 were recorded with the Position and Orientation Systems for Marine Vessels (POS-MV) and C-Nav Differential Global Navigation Satellite System (DGNSS) Precise Point Positioning systems. Two sets of controlled data are provided for each year of expedition. The first set is at time intervals of seconds for every day of the cruise and the second set is at 15 minute intervals. The data consist of Latitude, Longitude, Heading, Roll, Pitch, Heave, Track, Speed and Global Positioning System (GPS) sources at the second time intervals. The vessel's tracks in .kml (Google Earth format) were derived from the 15 minute time intervals dataset and are also provided. Data before 2020 are presented in INT format; an internal text based format adopted by ArcticNet since the 2003. For the year 2020 and afterward, Amundsen Science has adopted CSV (Comma Separated Value) format to support its new policy on Open Data and Open Science. The corresponding ship tracks are presented in .gpkg (Geopackage format: https://www.geopackage.org/) after 2020. Research programs participating in the Amundsen expeditions between 2003 and 2017 were CASES, ArcticNet, IPY-CFL, Solas, Geotraces, Malina, IOL and BP, Jamstec, Netcare, Weston, BREA, iBO and GreenEdge.